A multi-agent based system is proposed to simultaneous scheduling of flexible machine groups and material handling system working under a manufacturing dynamic environment. The proposed model is designed by means of methodology and programmed in agent based systems development environment. Each agent in the model is autonomous and has an ability to cooperate and negotiate with the other agents in the system. Due to these abilities of agents, the structure of the system is more suitable to handle dynamic events. The proposed dynamic scheduling system is tested on several test problems the literature and the results are quite satisfactory because it generates effective schedules for both dynamic cases in the real time and static problem sets. Although the model is designed as an online method and has a dynamic structure, obtained schedule performance parameters are very close to those obtained from offline optimization based algorithms.